2. AP Biology 2005-2006 What do you notice about these phrases? radar racecar Madam I’m Adam Able was I ere I saw Elba a man, a plan, a canal, Panama Was it a bar or a bat I saw?

3. AP Biology 2005-2006 Chapter 20. Biotechnology: DNA Technology & Genomics

4. AP Biology 2005-2006 The BIG Questions…  How can we use our knowledge of DNA to:  diagnose disease or defect?  cure disease or defect?  change/improve organisms?  What are the techniques & applications of biotechnology?  direct manipulation of genes for practical purposes

5. AP Biology 2005-2006 Biotechnology  Genetic manipulation of organisms is not new  humans have been doing this for thousands of years  plant & animal breeding

6. AP Biology 2005-2006 Evolution & breeding of food plants Evolution of Zea mays from ancestral teosinte (left) to modern corn (right). The middle figure shows possible hybrids of teosinte & early corn varieties

7. AP Biology 2005-2006 Evolution & breeding of food plants  “Descendants” of the wild mustard  Brassica spp.

8. AP Biology 2005-2006 Animal husbandry / breeding

9. AP Biology 2005-2006 Biotechnology today  Genetic Engineering  manipulation of DNA  if you are going to engineer DNA & genes & organisms, then you need a set of tools to work with  this unit is a survey of those tools… Our tool kit…

10. AP Biology 2005-2006 Bioengineering Tool kit  Basic Tools  restriction enzymes  ligase  plasmids / cloning  DNA libraries / probes  Advanced Tools  PCR  DNA sequencing  gel electrophoresis  Southern blotting  microarrays

11. AP Biology 2005-2006 Cut, Paste, Copy, Find…  Word processing metaphor…  cut  restriction enzymes  paste  ligase  copy  plasmids  bacteria  transformation  PCR  find  Southern blotting / probes

12. AP Biology 2005-2006 Cut DNA  Restriction enzymes  restriction endonucleases  discovered in 1960s  evolved in bacteria to cut up foreign DNA (“restriction”)  protection against viruses & other bacteria  bacteria protect their own DNA by methylation & by not using the base sequences recognized by the enzymes in their own DNA

13. AP Biology 2005-2006 Restriction enzymes  Action of enzyme  cut DNA at specific sequences  restriction site  symmetrical “palindrome”  produces protruding ends  sticky ends  Many different enzymes  named after organism they are found in  EcoR I, Hind III, BamH I, Sma I Madam I’m Adam CTGAATTCCG GACTTAAGGC CTG|AATTCCG GACTTAA|GGC  

14. AP Biology 2005-2006 Discovery of restriction enzymes 1960s|1978 Werner ArberDaniel Nathans Hamilton O. Smith Restriction enzyme movie Restriction enzymes are named for the organism they come from: EcoR I = 1st restriction enzyme found in E. coli

15. AP Biology 2005-2006 AATTC GAATTC G G G G G CTTAAG GAATTC CTTAAG CTTAA CTTAAG DNA ligase joins the strands. DNA Sticky ends (complementary single-stranded DNA tails) Recombinant DNA molecule AATTC G G CTTAA Biotech use of restriction enzymes Restriction enzyme cuts the DNA Add DNA from another source cut with same restriction enzyme

16. AP Biology 2005-2006 Paste DNA  Sticky ends allow:  H bonds between complementary bases to anneal  Ligase  enzyme “seals” strands  bonds sugar- phosphate bonds  covalent bond of DNA backbone

17. AP Biology 2005-2006 Copy DNA  Plasmids  small, self-replicating circular DNA molecules  insert DNA sequence into plasmid  vector = “vehicle” into organism  Original plasmid is call a cloning vector  transformation  insert recombinant plasmid into bacteria  bacteria make lots of copies of plasmid  grow recombinant bacteria on agar plate  clone of cells = lots of bacteria  production of many copies of inserted gene DNA  RNA  protein  trait

18. AP Biology 2005-2006 Recombinant plasmid  Antibiotic resistance genes as a selectable marker  Restriction sites for splicing in gene of interest Selectable marker  Plasmid has both “added” gene & antibiotic resistance gene  If bacteria don’t pick up plasmid then die on antibiotic plates  If bacteria pick up plasmid then survive on antibiotic plates  selecting for successful transformation selection

19. AP Biology 2005-2006 Selection for plasmid uptake  Ampicillin becomes a selecting agent  only bacteria with the plasmid will grow on amp plate LB/amp plateLB plate all bacteria grow only transformed bacteria grow

20. AP Biology 2005-2006 Need to screen…  Need to make sure bacteria have recombinant plasmid plasmid amp resistance LacZ gene restriction sites lactose  blue color recombinant plasmid amp resistance broken LacZ gene lactose  white color X inserted gene of interest origin of replication all in LacZ gene EcoRI BamHI HindIII

21. AP Biology 2005-2006 LacZ is a screening system XX  Make sure inserted plasmid is recombinant plasmid  LacZ gene on plasmid produces digestive enzyme  lactose  (X-gal)  blue  blue colonies  insert foreign DNA into LacZ gene breaks gene  lactose (X-gal)  blue  white colonies  white bacterial colonies have recombinant plasmid We want these!!

22. AP Biology 2005-2006 Amp selection & LacZ screening - gene of interest - LacZ gene - amp resistance LB/ampLB/amp/Xgal

23. AP Biology 2005-2006 Gene cloning Recombinant DNA movie

24. AP Biology 2005-2006 Cut, Paste, Copy, Find…  Word processing metaphor…  cut  restriction enzymes  paste  ligase  copy  plasmids  bacteria  transformation  PCR  find  Southern blotting / probes

25. AP Biology 2005-2006 Any Questions??

26. AP Biology 2005-2006 Chapter 20. Biotechnology: DNA Technology & Genomics Part 2

27. AP Biology 2005-2006 What if you don’t have your gene conveniently on a chunk of DNA ready to insert into a plasmid? Have to find your “gene of interest” out of the entire genome of the organism…

28. AP Biology 2005-2006 DNA libraries  Cut up all of nuclear DNA from many cells of an organism  restriction enzyme  Clone all fragments into plasmids at same time  “shotgun” cloning  Create a stored collection of DNA fragments  petri dish has a collection of all DNA fragments from the organism

29. AP Biology 2005-2006 Making a DNA library 1 all DNA from many cells of an organism is cut with restriction enzymes all DNA fragments inserted into many plasmids engineered plasmid with selectable marker & screening LacZ gene gene of interest clone plasmids into bacteria

30. AP Biology 2005-2006 Making a DNA library 2 recombinant plasmids inserted into bacteria gene of interest bacterial colonies (clones) grown on LB/amp/Xgal petri plates But how do we find colony with our gene of interest in it?

31. AP Biology 2005-2006 Find your gene in DNA library  Locate Gene of Interest  to find your gene you need some of gene’s sequence  if you know sequence of protein…  can guess part of DNA sequence  “back translate” protein to DNA  if you have sequence of similar gene from another organism…  use part of this sequence ? Which bacterial colony has our gene?

32. AP Biology 2005-2006  DNA hybridization  find gene in bacterial colony using a probe  short, single stranded RNA or DNA molecule  complementary to part of gene of interest  tagged with radioactive P 32 or fluorescence  heat treat genomic DNA  unwinds (denatures) strands  DNA hybridization between probe & denatured DNA Locating your gene of interest 5’ 3’ labeled probe genomic DNA GATCAGTAG CTAGTCATC

33. AP Biology 2005-2006 Hybridization Cloning - plate with bacterial colonies carrying recombinant plasmids 1 2 Hybridization - heat filter paper to denature DNA - wash filter paper with radioactive probe which will only attach to gene of interest Replicate plate -press filter paper onto plate to take sample of cells from every colony 3 Locate -expose film -locate colony on plate from film 4 film filter plate plate + filter

34. AP Biology 2005-2006 Problems…  A lot of junk!  human genomic library has more “junk” than genes in it  Introns, introns, introns!  if you want to clone a human gene into bacteria, you can’t have…. introns

35. AP Biology 2005-2006 Solution…  Don’t start with DNA…  Use mRNA  copy of the gene without the junk!  But in the end, you need DNA to clone into plasmid…  How do you go from RNA  DNA?  reverse transcriptase!

36. AP Biology 2005-2006 cDNA (copy DNA) libraries  Collection of only the coding sequences of expressed genes  extract mRNA from cells  reverse transcriptase  RNA  DNA  from retroviruses  clone into plasmid  Applications  need edited DNA for expression in bacteria  human insulin

37. AP Biology 2005-2006 Southern Blotting  Through a series of steps, DNA that has been separated by electrophoresis is applied to a membrane of nylon or nitrocellulose.

38. AP Biology 2005-2006 PCR  This is the polymerase chain reaction. It is a technique to multiply a sample of DNA many times in a short period of time. It supplies the scientist with sufficient DNA for further testing.  http://wps.prenhall.com/wps/media/objects/487/ 498929/CDA12_2/CDA12_2a/CDA12_2a.htm http://wps.prenhall.com/wps/media/objects/487/ 498929/CDA12_2/CDA12_2a/CDA12_2a.htm

39. AP Biology 2005-2006 PCR

40. AP Biology 2005-2006 DNA fingerprinting (RFLP analysis)  RFLP is restriction fragment length polymorphism. This is the idea that each person’s DNA would cut up into different sized fragments. Thus the pattern produced by electrophoresis of those patterns would be unique to the person.  Often probes are used to detect specific fragments, so the pattern is not so “crowded” to see.

41. AP Biology 2005-2006 DNA fingerprinting (RFLP analysis)

42. AP Biology 2005-2006 Any Questions??